Like any commercial aircraft AF Two must be visible to and under the control of FAA ATCs. Those radio transmissions are on public frequencies.
AF One and Two also have encrypted radio capabilities. In a wartime situation, you won’t be able to listen in without the same equipment and the cryptographic key of the day.
Somewhat related, in the same scenario, your GPS devices are going to be wildly inaccurate, unless, again, you have a military receiver with the cryptographic key of the day. (this is designed to prevent enemies from using known GPS coordinates to target US interests)
Doubtful they would have e gaged wsrtime comms on the trip up to NH before the emergency. AF2 would have been visible to anyone who wanted to fi d it. As for trip back, destination was announced as DC and Pence seen entering WH. That fact would show no use of secure comms as destination was announced znd followed through.